We will arrive mid- October in Venice for an unexpected 5 day stay. In looking at Ricks guide there are lots of possibilities for day tours. Are we advised to pre-book tickets for museum entrance, gondola rides, guided bus tours or are the crowds gone at that time of year?
You will be hard put to find bus tours in Venice no matter what time of year.
If you are planning on lots of museums, the pass that gives you one entrance at all the main museums can be a good deal, especially if you are there for 5 days. There is no need to pre book a vaporetto pass, the 7 day one will work best, and you can add on the bus trip to and/or from the airport for a small discount.
The best day tours are ones you do on your own. Download the Grand Canal RS audio guide and ride the No 1 vaporetto starting at Piazzale Roma (so you get first dibs on the best seats), and ride to RS's own narration.
Use the vaporetto to do day trips to Murano, Burano, Torcella, and other islands like San Giorgio, Cimitera, and even Lido.
Crowds are ever present in Venice. But they will be all at Piazza San Marco, Riva Degli Schiavoni, and Rialto.
I've been there the last few years in early to mid October. There are still crowds, particularly if a big cruise ship is in port, but nothing like what I've heard described in the summer.
If you want to do the secret itineraries tour at the Doge's palace, I suggest booking that ahead. Booking a reservation time at San Marco via the Internet is really inexpensive so it might be worth doing it; I'm not sure how effective it is. Try to go when the mosaics are illuminated. I think it's around 11, but check their website. And avoid San Marco on Sunday (unless you want to go to Mass), since the open hours are very limited because of services.
Beyond that, I don't think you need to reserve anything. There are gondolas all over, so you can arrange that when you're there. You're not going to have much luck with a bus tour in Venice, since there are no roads or motor vehicles in the city. Context Venice does amazing walking tours. And there is a good Rick Steves audio tour of the Grand Canal that you can download for free.