This is a mild 'liberty 'as it involves already having a vaporetto ticket for the day (or  the more economic 3 day ticket).  One can then take Line aNord from Fondamenta Nove and cruise the lagoon out to Murano, Mazzorbo, Burano and Torcello - hopping off as the mood takes you - and not be tied to the regime of a tour party.  Admittedly. any entry fees are still liable, but this method allows for a more flexible approach.  This still includes those amazing views of the city from the lagoon which may otherwise be missed.  Early evenings has the best light and can be a little cooler, perhaps take a jacket if out of the main summer season.  Though some attractions may not remain open late, so read your guide book first and get the best out of a low cost half day or more!  It's quite possible you may spend longer than you originally may estimate. 

None of the vaporetto lines currently go through any part of the important historical naval yards of the Arsenale. The nearest you can get by vaporetto is either the No 1 or 41/42 which call at the Arsenale landing stage close to the entrance to the Rio dell' Arsenale or the 51/52 line which calls at S. Pietro or,  on the northern shore, both the 41/42 and 51/52 call at the Bacini landing stage.