I don't know if there is really a "best". Sure some lenders have additional overlays, but I would recommend that you ask friends who they've had good luck with. I'm in the process of buying my first home, and honestly I've found the mortgage process to be really easy - now the building a new home part has been a cluster, but the mortgage part has been simple. I applied with NFCU in person and with the builder's preferred lender as well. I was able to meet with both people face to face, and I think that really helped. I'm not sure I would like a fully-online environment for something as complex and long-term as financing a house.
For what it's worth, in my case, the builder's preferred lender terms were nearly identical with NFCU. I ended up going with the preferred lender because she followed up with me a few times before I made a decision, versus the NFCU rep did not follow up with me once.