It sounds like you may have made your choice but I’ll add my two-cents because we were booked for one and stayed at the other. We were on a RS tour that was booked for the Hotel des Alpes. Our plan is always to arrive a few days ahead of a tour and stay at the tour hotel for convenience. Hotel des Alpes was booked up, so we made a reservation at Beau Sejour based on reviews and cost. They were lovely to work with, especially after the 2 days opened up at des Alpes and we cancelled.
The location of des Alpes was a key for us because of its proximity to the train station and city center. We were never bothered by noise and 2 of our rooms fronted the river. There was no AC, but Dyson fans in each room. We were given vouchers for breakfast. We were able to walk from the train station to the hotel.
We ended up walking by the Beau Sejour during a lake stroll and a bus ride to the Transport Museum. From the outside, the interior looked lovely and it’s across the street from the park along the river. It is a substantial walk from the main center, but a bus runs along the street in front and your hotel gives you a free transit pass.
Hope this helps