You can't say "pay by money". "Pay with money" is OK, but in practice you'd always say "pay with/by cash", "pay with a cheque/card", "pay by cheque/card" or whatever.

You can say 'pay with cash' or 'pay by cash'.

"Pay by/wish cash" is correct and more natural sounding than "pay with money", although as Victoria said, that is certainly another option. You can always just ask, "What methods of payment do you accept?" to avoid the money/cash vocabulary issue though. :)