I'm a writer, and after I put together my proposal I felt that maybe I should look into the world of LDS publishing because of the subject matter in my book. Which is the best publisher for LDS authors?
First, if it's fiction, you'll need more than a proposal. You'll need the full manuscript. If it's non-fiction, a proposal may be enough (check the publishers' websites for submission guidelines) but you'll need to be able to show sample chapters soon after, if they're interested.
Now for the rest of your question. It depends on your book, it's content, and what you want to do with it.
Deseret Book is generally considered the "best" publisher for LDS authors of books with LDS content because they've been in business the longest. They are very well established in the minds of the customer and they have a reputation for good products. They also have the largest distribution network for LDS books AND a zillion of their own stores.
For getting your book on LDS bookstore shelves and in front of the LDS reader, Deseret Book is arguably the "best"—if they accept your book.
But. Here's the downside.
Because DB is at the top of the list in the minds of most LDS authors and readers, they also receive the most submissions and, therefore, send out the most rejections. The competition for acceptance at DB is fierce.
After an author is rejected from Deseret Book (I'm not saying that you WILL be rejected, just talking probabilities based on numbers), there are quite a few other LDS publishers to consider. I am not going to recommend any here. You need to do your own research.
Start by Googling "LDS Publishers" and see what pops up. Talk to published LDS authors about their experiences—which publishers they'd recommend and which they didn't care for. Then find a match for you and submit!