Good lighting is essential, so try and go when it's sunny, and obviously several visits might need to be made at various times of the day to get the sunlight coming through the stained glass windows. A monopod/tripod will help, but ask if they'll be ok to use, otherwise just try out the higher ISO settings.
If you ask the vicar/priest/chaplain etc., they'll often advise when there'll be fewer people about. They might even say that you could make an appointment and they'll open the church for you and give you a "tour" and some historical info (if you like that sort of thing), a small donation to the church would be nice gesture if they do that, but up to you.
Generally don't photograph people in there if they're praying or in a service.