To me the obvious reason is the null hypothesis: in the US law enforcement officers don't actually have the standard operating procedure of "putting a few bullets" in people for "resisting arrest". The alternative hypothesis is a double conspiracy theory, that they are generally cold blooded killers, but in this case for some whatever reasons, they didn't shoot the Boston bomber, but rather they kept him alive to make an example out of him? I don't know, this doesn't pass any type of smell test to me.
No the reason is basically that he didn't move. If SWAT is on your front lawn and you walk out the front door expect a swift death even if you are innocent and completely unarmed. Curl down and hide in a way that makes you completely defenseless? Well first of all they don't have 5 marksmen pointing their gun at you in anticipation because they have to find you first and second they actually have an opportunity to arrest you because you're not running away from them.
I was citing "reason" as in "reason he was taken alive".
I said luck, because not much beyond plain luck allows you to survive 110+ rounds fired into the relatively small fiberglass boat you are hiding in. Not moving might have helped, but there's still quite a but of luck there. He had at least three serious bullet wounds.
[1]https://pixel.nymag.com/imgs/daily/intelligencer/2013/04/22/...