You have a difficult search on your hands! First, I am finding that it was not uncommon, especially for someone who did not want to be found (such as a runaway) to join the navy under an alias. In such cases, tracking the individual will be difficult...and it would have been difficult for the individual to collect a pension, etc. in later life!
Secondly, it would have been unlikely for him to have fought in the war. He would have had to have stated that he was 18...a stretch for a 12 year old. The navy, like the army, had a vast surplus of volunteers (something we would find surprising today...in 1898, the army, for instance, was being forced to take thousands more men than it needed. These men, never needed to begin with, languished in camps and faced death by disease through unsanitary conditions and overcrowding).
He could have claimed he was 14. At 14, he would have been accepted into the naval apprentice program. However, apprentices received two years of training onshore before being placed in a crew (yes...that makes it possible for a crewman to be 16, but only if he sported the insignia of a naval apprentice).
Could he have gotten into one of the naval milita groups? Possibly...their rules may have been less stringent, and Massachusetts had a naval militia. This would also make sense in that his father found him. The militia came home after the war. If he was in the actual navy, his father may have had to travel around the world to get him. The news that he was in the miitia would have leaked out easier, since the group was made up of locals...not men from all around the world, as was the U.S. Navy.