The advice from most of this board will be to visit the Thermo and Waters demo labs with replicates of the same sample(s), your column and necessary mobile phases and ask each to run the analyses (as it is doubtful that any lab would buy one of each instrument and be able to give you direct comparative information).
Having both instruments analyze identical samples will get you a direct comparison relavent to your needs. If you're making a large item purchase such as this there is no better way to make an informed decision.
Relying on the opinion of others can lead to disappointment on the majority of occasions.