I just purchased a cover for a jeep yj from 4wheelparts.com. They have a lot of stuff that is not listed on their web site but you can call their toll free number as ask if they carry covers for the cherokee. It arrived about 3 days after I ordered it. Works great.
2000 Jeep Grand Cherokee V8 Stock
93 YJ I6 hard top (really belongs to SPEED)
RE 4.5" Extreme Duty Lift, Advanced Adapters SYE, Tom Woods CV Drive Shaft, EA589 10" rims with 33" x 12.5" MT/Rs
Bullet Proof Front and Rear Bumpers and Tow bar