For Venice the place to go (for the best coffee in Venice) is Torrefazione Marchi at Fondamenta dei Ormesini, 2804 in the Cannaregio district close to the Campo del Ghetto. The surrounding area is also a great place for dinner or bar hopping. Just walk by the fondamenta and pick your favourites. It is quite lively in the evening.
Caffe del Doge is another pretty good cafe near the Rialto bridge on a small alley called Calle dei Cinque. If you want coffee near the Rialto bridge or the market area, Doge is a safe bet to have a cup and give your feet a rest.
Of course the most famous cafe in Venice would be Cafe Florian at the Piazza San Marco. It is said to be the first cafe in Europe established in the early 18th century (1720 if I remember correctly). It may very well be the first cafe (since it is also said that coffee first came to Europe via Venice) and the interior is wonderful. But be warned, the prices may be steep. Especially on the terrace on the piazza. Usually there is also a band playing mediocre music on the terrace. You'll have to pay for that too if you want to sip your coffee on the terrace. Anyhow the real charm of the Florian is on the inside (unless someone absolutely loves sitting outside watching tourists taking selfies).
But if you want a bit of that old time charm, go boldly inside and feel the spirits of some historic persons who used to hang around there: Casanova, Charles Dickens, Lord Byron, Marcel Proust, Thomas Moore, Charlie Chaplin, Hemingway, Jean Cocteau, Claude Monet and even Andy Warhol to name a few. Today it's filled with tourists, but like I said, at least the interior is wonderful. For coffee I would always choose Marchi.