Did you use all butter? In my vast chocolate chip cookie experience (they're almost the only cookie I bake) butter only makes a flat cookie. Half or all shortening makes a puffier cookie.
I've been experimenting with half trans-fat free shortening and half butter. I've not gotten what I want yet. Crispy edges, the crackle edges on top, still gooey chips on the inside, but still a bit puffy.
I haven't used water with the baking soda. I do use extra vanilla, and I've never noticed the extra liquid making the cookies flat.
It is odd that your cookies are flat even with all that flour. Can you post the entire recipe?
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