There is a command specifically for sitting in a captain's chair. If you type "/emote sit" it should give you auto-complete options and it's in there somewhere, because I can't remember it off hand at the moment
Stand on the seat and face out. Back up until your feet drop into the chair (instead of hovering over it), then use the sit captain emote.
The first time or two I tried I found my character hovering over the chair. When I used the above method, it worked just fine. The key is, if the captain looks like he's standing in the air over the chair, he'll sit that way too. Make sure to position him so that his feet make contact with the chair.