All your choices are possible, and so is 'bigger' that you have in your header, and also 'larger'. Some people might prefer one or the other, but I personally have no strong preference. I might say any of them. Perhaps not 'bigger' so much; this is more suitable for physical sizes.
Note: The verb needs to be 'was' because you're talking about the actual number: this number was bigger than that number. (Contrast with 'a number of' when it means "many"; then the verb has to be plural: A number of students were late today.)
I would also leave out 'that'; it sounds rather stiff there. The number of students in 2006 was greater/higher/larger/bigger/more than in 2005.