barbecue - Carib barbricot
bayou - Choctaw bayuk
buccaneer - Tupi mocaen ‘grill for frying or curing meat’
cacique - Arawak kassequa ‘chief’
cacomistle - Nahuatl tlacomiztli
caiman - Carib acayuman
cannibal - Tupi caryba ‘superior man’
canoe - Caribbean
capybara - Tupi
caribou - Algonquian
carnauba [wax] - Tupi
cassava - Taino caçábi
cashew - Tupi acajú
caucho, Fr. caoutchouc - Quechua kawchu
caucus - Algonquian caucauasu ‘counselor’
cavy - Galibi cabiai, or perhaps Quechua qowi
cayenne - Tupi kyinha
chocolate - Aztec chikolatl possibly ‘water (made with a) chikol (stick)’
chayote - Nahuatl chayotli
cherimoya - Quechua chirimuya
chigger - Cariban chigo
chile, chili - Nahuatl chilli
chinchilla - Aymara chinchilla
chipmunk - Algonquian chitmunk
chunkey [game] - Catawba chenco
cigar - Maya sik’ar ‘smoke’
coati - Tupi coatí
coca - Quechua kuka
cocoa, cacao - Nahuatl cacahuatl (Note: French cacahuète is from Nahuatl tlacucahuatl)
coho [salmon] - Salish
condor - Quechua kuntur
copal - Nahuatl copalli ‘resin’
cougar - Tupi suasuarana ‘like a deer’
coyote - Nahuatl cóyotl
coypu - Araucanian kóypu
curare - Cariban kurari
dory - Miskito dóri
enchilada - ultimately from chile
Great Spirit - loan translation of Ojibwa kitchi manitou
grouper [fish] - Ge-Pano-Carib?
guacamole - Nahuatl ahuaca-molli ‘avocado sauce’
guano - Quechua wanu
guacharo - Quechua wachu
guarana - Tupi guaraná
gaucho - Quechua wakcha ‘poor person’
guava - Caribbean
guanaco - Quechua wanaku
hammock - Taino
high muckamuck - Chinook hiu muckamuck
hickory - Algonquian pawcohiccora
hoatzin - Nahuatl uatzin
hogan - Navajo hogan
hominy - Algonquian
how [greeting] - Dakota háo, Omaha hau
hurricane - Carib huracan ‘his one leg’ - the name of a god
husky [dog] - corruption of ‘Eskimo’, ultimately Algonquian
igloo - Eskimo iglu
iguana - Arawak iwana
Inca - Quechua inka
ipecac - Tupi ipe-kaa-guéne ‘medicinal plant’
jacana - Tupi-Guarani jasaná
jackaranda - Tupi yacarandá
jaguar - Guarani jaguá
jerky - Quechua ch’arki
jicama - Nahuatl xicamatl
kachina - Hopi qacina
kayak - Eskimo qajaq
kiva - Hopi
lagniappe - Quechua yapay ‘add, addition’
lima [bean] - Quechua rimay ‘speak’ (Lima, the city, is named after the river Rimaq, i.e ‘Speaking’)
llama - Quechua llama
macaw - Tupi macahuba
maguey - Taino
mahogany - of unknown origin, but the tree is Caribbean...
maize - Carib mahiz
malamute - Eskimo Mahlemut ethnonym
mangrove - Taino mangle
manioc - Tupi mandioca
maraca - Tupi
maté - Quechua mati
mescal - Nahuatl mexcalli
mesquite - Nahuatl mizquitl
moccasin - Natick mohkussin
mole - Nahuatl -molli ‘sauce’
moose - Natick moos
mugwump - Natick mugquomp ‘captain’
mukluk - Eskimo muklok ‘large seal’
muktuk - Eskimo maktak
muskrat - Natick musquash + ‘rat’
ocelot - Nahuatl ocelotl
opossum - Powhatan aposoum
papaya - Carib
paca - Tupi páca
pampa - Quechua pampa ‘flat’
papoose - Algonquian papoos
parka - Aleut parka ‘skin’ (< Russian < Samoyed!)
pawpaw - Carib (same source as papaya)
pecan - Algonquian paccan
peccary - Carib pakira
pekan - Abnaki pékané
pemmican - Cree pimikân
persimmon - Cree pasiminan ‘dried fruit’
petunia - Tupi petyn
peyote - Nahuatl peyotl
piranha - Tupi pirátsainha
pirogue - Carib
poncho - Araucanian pontho
pone - Algonquian äpân
potato - Taino batata
potlatch - Nootka patshatl
powwow - Algonquian
pulque - Nahuatl poliuhqui ‘spoiled’
puma - Quechua puma
pung [work sled] - Algonquian tom-pong
quahog - Narraganset poquaúhock
quetzal - Nahuatl quetzall
quipu - Quechua khipu ’knot’
quinoa - Quechua kinwa
quinine - Quechua kinakina
raccoon - Algonquian arathkone
sachem - Narraganset sâchim
saguaro - Pima
samp - Narraganset nasàump
sapodilla - Nahuatl tzapotl
sasquatch - Halkomelem sesqəc
savannah - Taino zabana
seapoose [riptide] - Munsee sepoûs
scuppernong - Algonquian (from a river name)
shack - Nahuatl xacalli ‘thatched cabin’
shark - Maya xoc
skunk - Massachuset squnck
squash - Massachuset askōōtasquash
squaw - Massachuset squa
sockeye [salmon] - Salish sukkegh, or Northern Straits Salish seqey’
sofkee - Muskogean safki
succotash - Narraganset msíckquatash
tamale - Nahuatl tamalli
tamandua - Tupi tamanduá ‘ant-catcher’
tamarack - Algonquian
tamarin [monkey] - Galibi
tanager - Tupi atá ‘walk’ + carâ ‘around’
Tanis - Cree ‘little daughter’
tapioca - Tupi tipioca ‘residue’
tapir - Guarani tapiira
teocalli - Nahuatl teocalli
teosinte - Nahuatl teocentli
tepee - Dakota thipi
terrapin - Algonquian *toolepeiwa
tinamou - Galibi tinamu
tobacco - Arawak tzibatl
tomahawk - Algonquian tamahaac
toboggan - Micmac tobākan
totem - Ojibwa nintōtēm
tomato - Nahuatl tomatl
tonka [bean] - Galibi
toucan - Tupi tucana
umiak - Eskimo
vicuña - Quechua wik’uña
wampum - Algonquian wampumpeage
wapiti - Shawnee wapiti ‘white rump’
wickiup - Fox wikiyapi
wigwam - Abnaki wikewam
Winona - Dakota Winũnã
woodchuck - Algonquian otchek
yautia - Taino
yucca - Arawak
Could uh-uh and uh-unh come from Cherokee? They’re Americanisms, and the former at least recalls the Cherokee negative, a nasalized high vowel. On the other hand, some have claimed an African origin for these expressions. And on the third hand— you need a lot of hands in philology— nasals with negatives and central vowels are suspiciously common across the world (like "mama" or "papa"), and are thus hard to attribute to borrowing.
Place names from Amerindian languages are legion; I’ll just note one: Chicago, from Menominee shəkããkw, the locative of ‘skunk’-- i.e. ‘skunk place’, according to Jim Fidelholtz; but others derive it from a Miami-Illinois word for ‘place where wild onions grow’.