I dunno 'bout Howland. He's got all the information that Eddard did not give us...
1) Lyanna Stark. What was the exact nature of her relationship with Rhaegar? How did she die? What did Eddard promise her?
2) Ashara Dayne. What was the exact nature of her relationship with Eddard? Was her suicide due to Ser Arthur's death, Eddard's marriage, or Jon's departure with Eddard?
3) Wylla. She suckled both Edric Dayne and Jon Snow, but why her? What was her relationship with Eddard?
If these questions are answered by Howland, then we'll know exactly who Jon is.
You can find lots of speculation regarding Howland Reed in the thread
"promise me, Ned" and "the value of Howland Reed".
Back to Tom, well, my only other thought (and this is absolutely crazy) is that he's already dead. Not undead like Catelyn, but murdered by a Faceless Man. I know it's ludicrous, but mayhaps Tom is actually been sent after Jaime, Jeyne, Robb's son, or the Blackfish.