I've visited exactly 285 zoos and 83 aquariums just in the United States and my choice as the all-time worst zoo that I've ever seen in America would likely be
Clay Center Zoo in Kansas.
The 'marquee' animal at Clay Center Zoo is an American Black Bear and it lives in a dank, grimy dungeon. Here is the entire exhibit:
American Black Bear Cage | ZooChat
Dishonourable mentions (in alphabetical order):
Alligator Alley - Wisconsin
Animal Gardens Petting Zoo - Wisconsin
Arbuckle Wilderness Park - Oklahoma
Bayou Wildlife Park - Texas
Bear Den Zoo - Wisconsin
East Texas Gators & Wildlife Park - Texas
Franklin Drive-Thru Safari - Texas
Gators & Friends: Alligator Park & Exotic Zoo - Louisiana
Glacier Ridge Animal Farm - Wisconsin
G W Exotic Animal Park - Oklahoma
Jo-Don Farms - Wisconsin
Northwest Arkansas Reptile Museum - Arkansas (now closed)
Olympic Game Farm - Washington
Sharkarosa Wildlife Ranch - Texas
Sierra Safari Zoo - Nevada
Special Memories Zoo - Wisconsin
Wild Wilderness Drive-Through Safari - Arkansas
Terrible Aquariums:
Beaver Springs Park Aquarium - Wisconsin
Morro Bay Aquarium - California (now closed)
National Park Aquarium - Arkansas
Roundhouse Marine Studies Lab & Aquarium - California
Seaside Aquarium - Oregon
Westport Aquarium - Washington