The title says it all. I am mostly certain that it was Beth “Beez” McKeever, but I have only the sound of the voice as my evidence.
At least according to the Mystery Science Theater 3000 wikia, you are not correct in your pre identification. That source gives the following timeline:
- Jann Johnson (1989-1990)
- Alexandra Carr (1990-1992)
- Mary Jo Pehl (1993-1997)
- Beth "Beez" McKeever (1997-1999)
Also, for Beth, her IMDB page under the Actress tab, shows several voices for MST3K including "Magic Voice" in the episode "The Deadly Bees" (1998), which would coincide with the above timeline, but postdates Mary Jo, rather than predates. In the linked article for Beth on the wikia, she also credits Mary Jo as her acting inspiration as "I just imagine what Mary Jo" would do.
The IMDB pages for Jann Johnson and Alexandra Carr, show them as "uncredited voice" for Magic Voice during their time when they were working on the series. So depending on which episode you are referencing, it would be either Jann or Alexandra doing Magic Voice.