EDIT: NEVER-MIND, missed your update that your solved your problem.
I mostly only use fusion/jazz sized toms, so if you're having trouble with a big 'ol 16" floor tom, YMMV (although i would think it's a must to close mic such a large tom).
Just reiterating a couple things that people here have already said:
-Hit harder, with control, making sure you strike the drum well.
-Go with at least a 5A stick. It's not a monstrous stick, but I find it's harder to get consistent tones with something smaller.
-Replace the heads. I wouldn't leave this as a last resort. Heads are very important. Fresh heads make a big sound difference. Single ply's (remo ambassador, evans G1) can help, but as bigtoe mentioned, may not be the sound you're after. I'm a big fan of G2s on the batter side, and G1s on the resonant side for the toms. But the G2 (or any double ply head) requires a good thwack to get a good tone from them that's not too damped.
What type of drums are you using? Are you doing a kick tunnel? I find that when I do a kick tunnel, or have any absorbent material right next to the drums, it dampens out my toms way too much if I'm just using overheads.
One last thing that may or may not work. I find that a room mic (even a crappy dynamic one) placed some where NOT along a wall can help pick up some of that initial high frequency hit, and helps bring more definition to the strike of the tom.
good luck
EDIT: NEVER-MIND, missed your update that your solved your problem.