I went to Venice in September last year - it was perfect weather wise, having been before in August and melted.
Get a vaporetto ticket for as many days as you are there and go everywhere on the vaporetto - much better than walking.
Of the lagoon islands, I would say Burano is a must see with the beautiful painted houses (and amazing Rosa Riva restaurant - have the risotto) and Torcello is fairly off the beaten track and has wonderful mosaics. Murano on the other hand is heaving with people and chockful of pretty horrible glassware, most of which comes from China.
Book tickets for things like the Doge's Palace and San Marco Basilica on line in advance - the queues are huge and not fun in the square with no shade. We did one of the guided tours of the Doge's Palace and it was well worth it.
At any time, Venice will be heaving with tourists but most of them don't leave San Marco - they want a gondola ride, a pizza, stand in St Mark's Square and they are happy. As soon as you go to Castello or Dorsoduro the numbers fade off a lot but the selfie sticks in San Marco can be overwhelming.
We stayed in an AirBnB in Castello - is was a v short walk from San Marco but v quiet and near a load of amazing restaurants. There is masses of bad food in Venice, but if you avoid pizza (not Venetian and no wood ovens due to fire risk) and San Marco, you will be on the right track. We liked having the ability to have an espresso and a croissant for 2 euros for breakfast every morning from our local cicchetti bar, rather than pay for an overpriced hotel breakfast.
If you want a concert with real quality musicians I would highly recommend Musica Palazzo. They perform shortened versions of popular operas in a faded palazzo which was hugely atmospheric. Seeing La Traviata there was superb.
Museum wise, Museum Correr, the Accademia, Ca Resonico, Peggy Gugenheim, Querini-Stampalia, Cini are all world class - it depends what interests you the most. However it is probably most fun going into churches or Scuolas to see art in its original settings.
For those must-sees would be the Frari, Scuola San Rocco, one of the big Palladio churches. My favourites would be the Scuola di San Giorgio degli Schiavoni - practically on your own with beautiful early pictures of George and the Dragon, and San Zaccaria - in a lovely piazza, again no crowds, just you and Bellini's masterwork.
If you've been elsewhere in Italy and got used to the fact that no-one goes to a restaurant before 8pm at the earliest, this is not the case in Venice! It's not really a late night town as most staff have to get the last train home to the mainland. If you go to a popular restaurant at 8:30 there won't be any tables. Helpfully there is no need to look glam (unless you want to) as absolutely everyone else you see is a tourist who has also been trudging about sightseeing in comfy shoes 
Finally - watch out if you are asthmatic. Venice is heavily polluted by all the diesel from the boats. We hadn't considered this and I was very wheezy by the time I got home.