I went to Chaya this weekend and had their vegan menu (set menu "A") and was quite impressed. It comprised of an amuse-bouche, a soup, starter, a couple of main dishes, brown rice or bread, your choice of dessert, and a drink (tea, coffee, rice/soy milk). The quality was high, and the quantity was sufficient. Good value. I'd definitely go back.

They also have a set menu "B" that includes seafood and is a bit more expensive (around 5300 yen), as well as a 'special dinner menu' that has 2 fewer courses (with a choice of starter and main dish) and is cheaper at around 3700 yen. You can also order a la carte.