Depends on your budget and what you want in your stay. Stayed In Sirmione this past September for 4 days. As mentioned above there is no train there, you go to either Peschiera Del Garda or Desenzano. From there you can take a bus to Sirmione, or a taxi or the ferry. I took the Ferry arriving but when we left we hired a taxi to drive back to the train station since it was a sunday and infrequent buses.
Sirmione itself is small and you can see the whole town in half a day. Peschiera Del Garda or Desenzano are larger. We choose Sirmione since it was smaller town to stay and still had the high speed ferry service. If you want a larger town go for either above. If you want quaint at night when all the day trip people are gone go Sirmione.
We stayed at Hotel Sirmione at the bottom of the island. If budget isn't an option go for one of the Termal resorts at the back of the island. Couple were 5 star places and amazing grounds.
We took the high speed ferry one day to Malcesine and the cable car to the top. Also had time to stop in Limone just across the lake for the day. Thanks to Roberto on this board for that one.
Another day we took the regular ferry to Bardolodino and walked around to a couple winerys up the hillside.
The link above has all the ferry times so you can see.