I believe you're better off shopping a book to agents first instead of publishers. A good agent will have contacts and know which editor in a publishing house would be right for your project. If you send it yourself, particularly if you don't know who to send it to, then the lowest level person in the publishing house, maybe even an intern, will read it. If they like it, it will be sent to someone else, but if they don't it will be sent back to you, and then you won't be able to resubmit it to that publisher (they keep records, and once they've bounced it, they won't look at it again unless it is considerably reworked). Also, some publishers aren't considering unagented or uninvited work.
The publishers are using agents, essentially, as their first readers. If an agent who has already sold books brings a new one, then the publisher knows that the agent, an experienced reader, is risking a part of his/her reputation on this new project. Not only will it go to the right editor, but it will also have the stamp of approval from the agent that it is a good, salable project.
There were a couple of years in a row where none of the major publishers accepted an unagented book. There have been a few since then, but an unagented sale, through the slush pile, is a rare event. (of course, all sales are rare events).
You probably do not need an agent, though, if you are approaching small press publishers, especially if it is a publisher that offers a small or no advance. Agents get a percentage of the advance, and if there isn't much of one, then they won't be interested. My sense of the small press world, though, is that it is much more contact driven. The small presses publish works by authors they already know and admire. I've heard very few stories of small presses publishing someone they didn't know beforehand. There are, of course, exceptions.
The old advice that you establish yourself in science fiction with a solid background of published short stories before trying to sell a novel is still good advice (if you can sell the short stories), but there are numerous authors who have never sold anything before selling their first novel. Starting with a book, then, is possible.
Writer Jeff Carver is wise about these matters at http://www.starrigger.net/published.htm