You really need to find out what the particular publishers you are interested in want. Some will only deal through agents. Some accept direct submissions. All of them have their own guidelines of what they would like to see first; chapters, a letter of inquiry or a whole book. The annual book Novel & Short Story Writer's Market can help you sort out those choices.

My own experience with dealing directly with a sci-fi publisher was fine. I sent one a very long novel. They responded quickly, and in a personal manner. I know from the things discussed in the letter that someone at the publisher read the whole thing. They told me what they liked and what they didn't. Since my novel's biggest problem is that it is way too long, I haven't tried too hard to sell it again.