See, one Hellpit is usually pretty easy to deal with for anyone prepared. Hell, even Wood Elves should nail it in a turn or two with a unit of Glade Guard with the Banner of Eternal Flame. As such, it's really a matter of two Hellpits or none, unless you're playing a game too small to fit a pair.
Another thing that's pretty common knowledge is that Warp Lightning Cannons are damn powerful. Top 5 Skaven units powerful. But then if you're taking your pair of Hellpits, you won't have any room for any Cannons until 2250 point games, and you won't be able to take a pair of them until 2600 points, which is a bit above the average (here at least). Thus, in my opinion, I think 2 Doomwheels and 2 Cannons is the superior option up until that level.
In terms of ranged fire power, 2 Cannons will mean fairly consistent firing, even when one screws up, as Skaven machines so often do, and, obviously, more dead stuff overall. I don't think I can adaquately describe the amount of damage a pair of Cannons has done for me, so I won't try. But you get the picture...
As for the Doomwheels, those things are insane. Some douche on the internet that clearly thought he was the lord of all Warhammer ever, told me that I must be using "better i.e. different" Doomwheels to the one's he's seen in his travels. That guy is either playing Dwarfs with as many War Machines as possible against opponents who don't bring a Storm Banner or, more likely, he's a moron.
The major benefit of Doomwheels though is their ability to wreck 3 machines, monsters, Ogres or what-have-you in a single shooting phase. I will admit that 3 Ogres isn't that impressive, but rolling up beside a Dragon, hitting it at S8 or 10, killing it with the first Zzzap! or two and then finishing off the rider with the third is always nice. Same with hitting 3 Cannons, Bolt Throwers or Catapults and taking them all out in one go with your relatively cheap Doomwheel. Then you can also fire whilst in combat and you completely ignore cover. Not much is really safe, provided you're in range. That includes your own slaves though, but they're slaves, so who cares?
In terms of survivability, the 4+ armour save is going to hold up much better against flaming attacks than the Regen the Hellpit relies on. Unfortunately Cannons are a pain, but that's what Gutter Runners and Storm Banners are for, and if they're not dead when you get close enough, your Doomwheels too.
2 Cannons and 2 Doomwheels will also annihilate enemy Hellpits you come across. They may not ignore the Regen, but they can only pass so many 4+ saves and when you're doing D6 wounds they won't be around very long. Or you could shoot them with Warpfire Throwers if you prefer, but that's going a bit off-topic.
Anyway, that's just what I've found with my experiences with Skaven. If people around your store don't have flaming attacks or lots of multi-wound shots, then do what you want. I just feel that 2 Doomwheels and 2 Cannons is stronger that 1/2 Hellpits and 2/1 Cannons.