Whether or not he's treated as an enemy combatant will be an interesting decision.
He's a US citizen. So my first inclination would be that he should be treated as such and be given a regular trial with all the standards of evidence and guilt that US citizens receive. I'm sure the ACLU will be screaming from the top of their lungs for this. This would be the Timothy McVeigh scenario.
However, if the investigation shows there are connections (most specifically aid and training) to a foreign terrorist organization, say Chechen jihadist organizations, than there is a really good argument to consider them foreign combatants.
To give you an example, if you watch the excellent show The Americans, the married couple in the show are US citizens...but they are KGB sleeper agents who are murdering people and bombing things, they're not REALLY US citizens. If they are caught on the show, they would probably be treated not as US citizens, and not as POWs protected by the Geneva convention, but as spies.
A major difference between the spies on The Americans and the Boston Marathon bombers, are that the TV characters are technically illegal aliens. This Dzhokhar Tsarnaev is a naturalized US citizen. If I were the government though, depending on the timing of his radicalization, I would argue that his naturalization last year was under false pretense, that he was taking the Naturalization Oath of Allegiance to "Support and defend the Constitution and laws of the United States against all enemies, foreign and domestic," with the knowledge that he was an agent of violent jihad against the US.
Either way, it won't end well for him.