Based on my Single player testing, yes it does increase your heavy melee damage.
Tested this by doing the following:
Vanguard with all relevant powers maxed
Character with maxed fitness (including all of the possible melee damage buffs) and a stunner on my pistol (no melee damage armor). Facing a marauder (with full health and shields), I could kill him in one biotic charge followed by a heavy melee.
Followed by a vanguard with 0 melee focus
Character with 0 fitness, and no stunner or melee armor (meaning default melee damage). Facing a marauder (with full health and shields), I required at least 1 followup light melee swing after a biotic charge/heavy melee combo.
Testing specifically weapon mods, I got the following results:
Vanguard with minor melee buffs (the default ones, choosing all health/shields choices where possible) against Cerberus Centurions.
While wielding a shotgun without the blade attachment, one heavy melee would leave the centurion with 2 bars of shields left (from full health/shields)
While wielding a pistol with a +22.50% melee damage stunner, one heavy melee would leave the centurion with no shields and between full health and one bar of health damage.
This shows that weapon mods do improve heavy melee.
Note all tests were done in singleplayer, but I'm assuming multiplayer results will be the same.