Asked a similar question myself earlier this year and was given some great advice. That, and my own personal experiences, I'd have to say:
Stay at Sequoia Lodge.
SL has always been a popular place to stay. The general atmosphere, the staff and the relaxing theme make your experience wonderful. Although the hotel isn't massively "Disney Themed" to be fair, none of them are; the exception being The Disneyland Hotel. When I asked my question, the general consensus was that there is just "something" about SL that pulls people in and I would have to agree with that completely. The Montana rooms in the main building are great if you don't mind paying slightly more for them over a standard room. If choosing a standard room, the Yellowstone Lodge is the place to stay. Then again, you could opt to upgrade to the Golden Forest rooms, something that seems to be very popular on here. I personally haven't stayed in a GF room so I'm unable to give an opinion there, however they come highly recommended by forum users.
Then there is the Newport Bay Club. I've never liked the hotel. I, like some others, feel that it is missing something. The rooms always felt odd and dreary. Getting to some rooms in the hotel always seemed to take ages and involved walking through more and more corridors with the same plain and boring decor. That is how I felt when we stayed there, though that is my own opinion and views. Many other people have stated they like the hotel.
My fiancee and I are going to Disneyland Paris in November. We initially looked at staying in Hotel Cheyenne to save money, however we opted to stay in SL instead as we wanted the use of a pool and I love the feel of the place. When we went to make the booking for a Montana Room, we discovered that the swimming pool was closed from November "until further notice". For us, this was a deal breaker. If you can live without the pool, I recommend still choosing SL. We really wanted a pool, so made our booking with Newport Bay Club instead. We knew that the refurbs were going on and had seen pictures of the new rooms which looked much, much better. The pool was also open so we decided to go for it.
A week or so after booking Newport Bay, we read that the refurb work being done was affecting some guests enjoyment. Most of the windows in one of the wings were covered with scaffolding giving little to no view for example and with one of the restaurants being closed, breakfast was a nightmare. Some guests complained that it was noisy, however I imagine that they were just looking to complain. When I asked our travel agent when the work would be finished, she told me next year at the earliest.
With the pool being closed, my past negative experiences and the refurb work being carried out, we decided to upgrade to Hotel New York.
So, if it wasn't for us wanting the use of a pool, we'd happily be staying in SL in a Montana Room. We were originally going to choose a lake view room, but after forum users advised us that at that time of year (November), you wouldn't see much anyway. SL at Christmas is also a fantastic experience and in my opinion, can rival even the Disney Hotel for atmosphere (prepare for incoming disagreements in 3... 2... 1... lol).
To sum up, I would highly recommend staying at SL anytime of the year, but even more so around Christmas time. Upgrading from a standard room to a Montana room is worth it but consider the time of year when opting for a lake view. If wanting the use of a pool from November however, look elsewhere. While the Newport Bay Club has a grand look, I couldn't recommend it myself. When the refurbs are complete, I would be interested in staying in one of the new rooms in the hopes that it changes my mind, but at this time, I couldn't recommend it.
I hope this somewhat helps you make a decision. If I can think of a few specific tips, I'll add them to the comments when I get home - currently typing this in between checking guests in

~ TappyFish~