Well you've got a few options here, I'll try to list them all.
1.
Coinbase - They offer direct integration with Shopify stores. It's pretty easy to set up and you can find instructions on the website I've listed.
2.
Bitpay - Also offers 1-click integration and this is probably the most popular solution for most merchants.
3.
Gocoin - A little bit more work to integrate into Shopify, but easy-to-follow instructions are available.
4.
Coinpayments (Bèta) - Easy integration into your Shopify store, but this gateway is still in bèta.
Those are all the Bitcoin gateways that I could find. I would definitely recommend going with either Coinbase or Bitpay, since they have the most established services.