There are many spots you can get this, since enemies tend to respawn immediately when you leave the screen they were on, so you can just turn back and kill them again, but here's how I did it:
Works with any gun, easier with Wave Emitter or Photon Launcher.
There's a long horizontal room that looks like a foundry or something - it's a red area with lots of junk in the background. Towards the end of the room, there's an area you can drop down into. Kill everything around the hole, drop down and head to the right while killing everything. Jump up and loop back to the left and you'll be above the hole again. Just loop over and over until you hit 99.
You can also use this area if you ever need to raise your total combo for level rankings. Any combo set during a play session carries over to all other attempts at all other levels, so you can just milk a high combo in an easy area like this one.