Which weapon out of all of them (besides missile launcher) has the highest damage per second( considering levels and charge)?
Simply put, the Spur has the overall highest DPS. Taken from here
The two highest DPS weapons are the Machine Gun, due to it's insane rate of fire (coupled with the TurboCharger nets you a faster reload, so more dps) and the Spur, that for a charge weapon, can easily do more damage than a few rounds of a maxed out machine gun.
Level 3: 6 damage, 10 xp to MAX. Ammo regenerates similar to level 2, hover/fly when shooting down. It is possible to float indefinitely.
Level 2: 15 damage, 60 xp to level up. Shoots stream. Unlikely you can pull off multiple. Goes through enemies if it kills them.
The neat thing about the Spur is that it only takes a few seconds to charge to max potential, much less if you need it at level 2. It also pierces enemies if it kills them, which means that even at Level 2, this thing can deal more damage than the machine gun.
The only reason you should ever consider taking the machine gun is for pure mobility.