What are the main reasons for choosing to pursue one over the other. Up until now, I have been considering querying agents. Maybe that is a poor choice.
In most genres, the best imprints offering the highest advances will only take agented submissions. If you submit directly, the door to those imprints is closed. As far as I know, your type of genre isn't one where major publishers take unagented submissions. An agent will negotiate your contract much better than you could, and get you a better deal. In return, she gets 15% of your royalties (20% non-domestic). Most agents are editorial and will work on making your manuscript the best it can be before submitting to publishers. They don't charge for this: agents make money when you do, and not before. Editors will usually prioritise agented submissions over non-agented, for those imprints where both are accepted. You'll likely move through the slush pile quicker. I can't really think of any cons for getting an agent. She takes 15% but should get you at least 15% more than you could get on your own. I suppose if you don't manage to get one, you lose a couple of months... but in publishing time, that's the blink of an eye anyway. But if you do query, make sure you do that BEFORE submitting to any publishers. Agents are generally not interested in manuscripts that have already been sent to publishers, unless it's been accepted (in which case she might be willing to step in and negotiate the contract for you).
That's very helpful information Tenderiser, thanks. I guess I better get busy with the query letter now. I have the first 6k words well edited now. From what you say this should be sufficient. If an agent likes that will they will help with editing the rest?
Nono. They're not free proofreaders! They'll only accept manuscripts that are final and polished. What I meant is they will give editorial feedback and work on fine-tuning things, not 84k of line edits. It's hard to get concrete stats but from what's out there, it seems that getting an agent is harder than getting a publisher. Most of them get 250+ manuscripts a week, and they will only take on a couple of new clients a year. You need to put your best foot forward.