2WD or 4WD? Automatic or manual? 4 cylinder or V6? I did some research, and according to Autozone.com it looks like if it's a manual for the 91 and 94 4X4 V6 manual both share a part number of W56-B. If it's an automatic, the part number is one off, A517502 for the 94 and A517501 for the 91, so I'm not sure if it's enough of a difference for it not to work.
Yes, a 1991 Toyota 4 Runner transmission will fit a 1994 Toyota 4 runner. This is because both models were made during the second generation of the car, which was from 1989 to 1995 and have the same transmissions.