Well, I suppose it all depends upon how a person looks at such things. If I were the boat owner, I wouldn't be looking for compensation from the city of Boston or the state of Massachusetts.
The cops, for once, were performing the fundamental task we've empowered them to do, which is, protect the public from harm. Yes, they could have tried to smoke the bomber out, coax him out, wait him out, etc., etc., etc. But in that highly charged and dangerous atmosphere, everyone just wanted the guy caught, and the threat ended.
For all anyone knew, he could have been holding a full auto rifle with a high cap magazine, ready to go out in a blaze of glory for Allah. He and his brother had already killed another officer, and of course, had killed and maimed people at the Boston marathon. In that moment, who knew what he might do?
Apparently, the boat owner is getting donations from all over the country to cover his financial loss. I think that's appropriate in this case. I don't blame the cops one bit for shooting up that boat, and I doubt the boat owner does either.