Lot's of things at play here. Ignoring what the overall environment of the area is (tropical, temperate, etc.), I would look at what makes sense given that giant rats under control of were-rats would likely be pretty much in charge. I wouldn't expect lots of competing groups, unless this is a huge sewer complex beneath a large and old city. I like to take inspiration from the real world as as starting point.
Starting with the rats, I would next ask what would likely live in the sewers to hunt the rats? Something that would be difficult for the were rats to eradicate? Regular and giant weasels, ferrets, and foxes; regular and giant centipedes, spiders, and scorpians; giant and regular fogs and toads. Not not everything needs to be giant. That can start to feel silly and a normal sized poisonous snake can be dangerous on its own. Snakes will use man-made structures like drain pipes and sewers as their hibernacula, so instead of a giant snake, you can have a party fall into a pit of hundreds of snakes.
I'm not a big fan of crocs and gaters in sewers, unless it fits with the surrounding environment.
What are things that rats may like to have around, say to hunt as food, that can still be dangerous? Like giant beetles for example.
For neutral yet creepy encounters spec out some funky worm monsters based on tobiflex worms, bryozoans, tubificids, etc. Oozes of course make sense.
Potential allies: lost pets like a dog may latch on to a party that treats it with kindness.
Don't forget some fun and silly flavor. In the real world, there have been goats and cows and such that fall into sewers.
If you want factions or powerful monsters that have stake out turf in the sewers despite the wererates:
- one or a small number of mind flayers who hid there after their colony was destroyed
- a Froghemouth that somehow got into the sewers when young and now too large to get out of a large cavernous area where it lairs. It is served by a fanatical group of bullywugs who worship it and bring it food, such as giant rats and foolish humans who wander into the sewers