Is that boat fairly light? The tow rating on a Tracker or Sidekick is only 1000lb.
If it is an aluminum fishing boat it can probably handle it, but a fiberglass runabout would probably be too much even for a 5spd.
I tow a small pop-up camper with my '96 16V 5spd Tracker that is probably about 1100 lbs with all the gear. It does ok on the prairie, but it struggles on the hills. I haven't towed with an automatic, so I really don't have any basis to compare, but based upon the performance of the 5spd, I would guess an automatic would really struggle to pull a boat. I think the 5spd would be less likely to fail due to the extra load, but that is just my opinion. I like the 5spd for its simplicity. It really isn't all that inconvenient to use as a commuter. I used my Tracker to commute 23 miles each way in the Chicago suburbs for years. You just get used to it...