-Hallockville Farm Museum (Riverhead)

-Barn at Old Bethpage Village Restoration (Bethpage)

-Bates House (Setauket)

-Peconic River Herb Farm (Riverhead)

-Spirit's Promise Horse Rescue (Riverhead)

-Salt Air Farm (Cutchogue)

-Dart's Tree Farm (Southold)

These places are all great for a rustic wedding! Also, many of the vineyards out east have a rustic feel. If you want the wedding IN the barn, it's usually a max capacity of 100-150 people, which is why some of these other places without a barn (or just a small barn for pictures) are great choices for larger weddings. 

Also keep in mind that most of these places are outdoors, so you'd need a tent. And all are pretty much DIY (you will need to bring in your own caterer- I HIGHLY recommend Moriches Caterers - the food is amazing and Anthony is always there to help with the planning and takes care of all the set up and coordination day-of).

Also, I was looking for a rustic barn wedding too, but ended up choosing Brecknock Hall in Greenport. It's an elegant estate, the wedding is tented outdoors, but there's a small barn and glass green house for rustic pictures. Perfect mix of rustic-meets-elegant. 

Sorry this is long but I hope it helps!