I also add my vote for a runabout. And I'd put holo emitters in the aft cabin.
This.... and an EMH equipped Sickpod for emergencies.
Runabouts were modular, so all 4 of the cabin areas could be swapped out for mission specific things. A holo med pod wouldnt be out of conceivability.
Not sure why you'd need a dedicated med pod if you've converted one of the cabins into a mini holodeck - you just just simulate the sickbay in there whenever needed.
I'm also not sure the computer in a runabout would be powerful enough to run the Doctor - the implication on Voyager (I feel so dirty right now using that as a reference, but oh well) was that he was unable to leave the ship at all, except to another full starship, until he got that far future-tech holoemitter. Unless, of course, those are the type of holoemitters we're talking about. Then, no problem.
One problem you probably wouldn't have is diverting enough power to run it - in the real universe, you're likely to VERY rarely need phasers or more than minimal shields. Only on the rare occasions where you need to keep a meteorite from hitting Earth er sumtin.