You've nothing to lose by asking. If you say to them you are also looking elsewhere but you like the look of their hotel better they may do you a deal or upgrade your room for the same price - speak to the Manager or reservations Manager if you can or email them - tell them that you found their hotel with Thomson but you'd much rather deal direct. IME Thomson will be paying considerably less than 490 euros for the week - possibly as little as a third of that!
I've had varying success when trying to do deals with hotels- Chain hotels are notoriously difficult sometimes, but some do follow the "bums on seats" rule (as do I with my own holiday business) and let at a discount rather than be empty. Remember you can always just walk away from the negotiation.