We use Brightpearl which is quite a lot more money monthly but gives you the abilty to sync multiple online stores alongside ebay stores and bricks and mortar. We currently run two Shopify stores and one on ebay but we went with this option as it is scaleable. Brightpearl handles real time inventory and accounting.
Brightpearl were really good throughout the setup process and after sales has been good, details here.
Let me know if you go ahead, if I refer you I can get you 10% discount and a free month for myself.
On the pure accounting side of things I have previously used
Xero was my favourite by far, really user friendly (I never used it for inventory)
Hope this helps, good luck