IDW have both Trek and Who comic licences, and it seems somehow they've managed to Make This Happen.
RTD thought/joked about crossing over when Enterprise was still on the air.
(Similarly, the Daleks were almost the secret rulers of the Federation in Blake's Seven but then weren't. David and Billie appearing in an issue of Buffy season eight doesn't count. And let us not speak of Dimensions In Time.)
One thing to be noted is that crossing over with the Whoniverse can be rather unbalanced as it can swallow most other settings whole. The same central character has seen the beginning and end of this universe and visited others as well. A century of heroic space exploration that starts a couple hundred years in the future? That's nice, nothing special, sounds like the backdrop for an episode, maybe two tops. And that's a pretty big setting too, most are confined to a single planet and a decade or so of activity.
An official crossover, rather than an expy that uses the heart of a setting as a plot hook for one night only, would probably be like a respectful Celebrity Historical, with the Doctor being impressed by the heroic guest stars as he helps them deal with a threat that could come from either universe. We shall see, of course.