We visited Venice for 3 nights in May and stayed at Rick's recommended Pensione Guerrato. Unfortunately it rained most of the time, but hey, we were in Venice! Pensione Guerrato was a fine place to stay, though a little gloomy (partly because of the weather).
A tip if you are staying at Pensione Guerrato -- if you are carrying luggage, be sure to get off at the Rialto Mercato stop as their directions tell you, not the Rialto stop. We took the Alilaguna boat into Venice from the airport -- they told us it didn't stop at Rialto Mercato, only Rialto, and we thought it wouldn't be a big deal. Turns out it was. The Rialto stop is on the other side of the canal from Pensione Guerrato, which means you (and your luggage) have to walk across the Rialto Bridge. Not fun to do dragging suitcases through a crowd of tourists, and not a good introduction to Venice. If you get off at Rialto Mercato, all you have to do is walk through an arch and you're practically at the hotel.
But things got better from there! St. Mark's is amazing and we went to a lovely organ concert in another church. Taking the vaporetti was fun once we got the hang of it. Venice is definitely a city better seen in sunlight, not gloom and pouring rain. But we're glad to have been there.