Yes, you can do either first.
The Sewer of Horrors was added after the Ark as a bit of an end-game challenge, but a lot of players take on the Sewers on before going to the Ark. There's a lot of nifty stuff in the Sewers (items, tombs, etc) but it is a long dungeon.
Depending on your level of difficulty, experience as a player, and character class and build, you might find the Sewer of Horrors a bit too hard before level 15 but if you're in the 18 to 20 range, it might be worth taking a shot.
Using out-of-game knowledge makes the Sewers a lot easier, so if you want an authentic challenge, take it on using just in-game knowledge. The Wiki can help if you have questions, or get stuck.