Doing a bit of quick napkin math for direct damage comparison using tooltip info from the poi, on an engie using a marauders amulet and hoelbrak runes in SPVP (ignoring vuln, might random procs, traits etc for now):
TL:DR, hammer and toolkit auto appear roughly equivalent.
Hammer autoattack chain base damage:
Positive Strike – 628 (.5 cast)
Negative Bash – 628 (.5 cast)
Equalizing blow – 807 (.5 cast)
Total in 1.5 seconds 2063 damage, or approx 1376 DPS.
For comparison in the same period of time:
Rifle:
Hip Shot: 591 (.75 cast)
Total in 1.5 seconds 1182 damage, or approx 788 DPS
Bombkit:
Bomb: 988 (.5 cast)
Total in 1.5 seconds 2964, or approx 1976 DPS
Toolkit:
Smack: 632 (.5 cast)
Whack: 632.5 cast)
Thwack: 1383 (1.0 cast)
Total in 2 seconds 2647 damage (for comparison sake, 1985 over 1.5 s) or approx 1323 DPS
Grenade Kit:
Grenade: 261 x3 (.5 cast)
Total in 1.5 seconds 2349, or approx 1566 dps
Flamethrower:
Flame jet: 1780 (2.25 cast)
For comparison sake, 1,186 over 1.5 s, or approx 791 dps
Mortar:
Mortar Shot: 632 (.5 cast)
Total in 1.5 seconds 1896, or approx 1264 dps
Quick Summary:
Bombkit:1976 DPS
Grenade Kit:1566 dps
Hammer: 1376 DPS
Toolkit:1323 DPS
Mortar: 1264 dps
Flamethrower:791 dps
Rifle:788 DPS