Limited time for sightseeing. Which to visit?

neither

It depends. What do you want to see/do??

I would choose Bainbridge. The ferry ride over is shorter and the town is more scenic. I don't really think there is anything that would be a "must see" in Bainbridge, but I do think it is a lot of fun to get out on the Puget Sound. Plus, the views of Seattle on the return trip are lovely. If you have the time in your itinerary, I think its worth a trip.

Bainbridge is much prettier.

The half-hour ferry ride to Bainbridge Island gives great views of the Seattle skyline and, on a clear day, Mt. Rainier, the Cascades, and the Olympics.

The ferry lands in the little town of Clinton which has a couple good places for lunch.

HTTY--The town of Clinton is on Whidbey Island, on the Mukilteo run not on the Bainbridge run.

So true.

Just shows what a month in Italy can do to the Seattle born and bred brain.

The town is Winslow.

My favorite stop for lunch is Harbour Public House. Others like downtown's Cafe Nola, but it leaves me somewhat chilly.

Here's a good website re both:
http://www.visitkitsap.com/

If you like gardens, try to go to the Bloedel Reserve (north of Winslow - west of Clinton ... magnificent ... but reservations are required.
You can find info about them (and other things) at the above website.