Will the canal boat be operating at this time in december
According to the tourism website, no.
I wouldn't feel too badly about it, though. Although worthwhile to have done, we didn't think ours was all THAT. You'll have some nice canal experiences just walking along some of them. The one that starts at Jan van Eyckplein square was especially nice in the early mornings before the boats started running.
To get an idea of the possible weather in December, you can watch the 1st half of the film "In Bruges", it was filmed on location in Bruges/Brugge in March.