Pruning upright water shoots on a mature Bradley apple tree

Hi I have a large bramley that was very productive last year but  has very little fruit this year. It is full of the upright water shoots that I was unable to deal with last year and so are now strong 2 year old branches. The tree is overcrowded with them and needs thinning. I didn't want to prune them out in winter to avoid stimulating the tree to send up more water shoots ..... so is it the right time to do it now?