In looking at the Boston Duck Tours website, the abbreviated tours start at 3:00 pm. Normal tours start earlier. This may be something to consider when taking into account if you want to do this. Not sure how long you are in Boston.
You can find the in person tickets locations here
, and it is the first or second FAQ listed.
2007 - Majesty of the Seas
2009 - Enchantment of the Seas
2010 - Freedom of the Seas