I have been making training flights with my 737 ngx running from Montreal (CYUL) to kjfk.Since I do not know what runway I will be landing on when I take off from Montreal I leave it blank. The problem is that  by the time I hit the last waypoint in my FP I am unable to contact jfk via ATC to get the runway assignment. I have tried to tune the radios to the JFK ATIS station in advance but can not get in touch with them to find out which runways are open. I usually end up opening the map and selecting a runway and setting up the approach with the hopes that ATC will assign me that particular runway or that I will be able to ask for it as an alternate. I would really like to enter all this info way in advance instead of having to worry about changing all my settings at the last moment should my runway not be available. Is there a way to find out which runway I will be assigned well in advance?

You could infer which runway heading you'll be assigned at your destination by looking at the weather at your destination prior to departure. Typically you'll be landing into the wind. Are you using a weather add on or live weather updates of some sort?

Check Skyvector.com - the little colored METARs will show up at all the airports.  Usually it will help you know which ones are in use.  If you're on vatsim/online it might be more complicated because of certain real world configurations...  JFK has a site for online flying that shows their configs:

http://www.nyartcc.org/runway

You could infer which runway heading you'll be assigned at your destination by looking at the weather at your destination prior to departure. Typically you'll be landing into the wind. Are you using a weather add on or live weather updates of some sort?

Using rex plus so sometimes its just random weather and sometimes its live weather. 

You could also enter a navaid at the destination airfield in your fmc after your last waypoint, fly to that while you try to figure out which rwy to use.