From the way you have described it, I wouldn't pay anything more than $1k for it. You can't fix a cracked head w/sealant, and 3.0 heads aren't that easy to come by.
A used/rebuilt long block will run you about $1900, while a new one is about $2500. You can usually find used 3.0's on the 4x4 boards or craigslist for under $1k, but you may still have a problem w/the engine.
If you do locate a replacement head, figure about $500 for a shop to go through/rebuild both heads, about $200 for a complete gasket kit, and another $300 for new headbolts(must use new, you cannot re-use them), knock sensor and knock sensor wire, and any misc. items. I would also consider pulling the block and having it bored 0.20-0.40 over, possibly enlarge the valves(though not a lot of room), and definately run a set of Downey headers to get away from the crappy stock x-over pipe, so figure another $700-800 for headers/exhaust, a 2" body lift(make installing the headers a lot easier and allow for more heat clearance, and heat shielding for the starter.
If it is an auto, you will probably want to swap in a 5-spd, the 2nd gen Runner w/3.0 is a gutless turd. So for about $3500(including the $1k purchase price) you would have a fresh 3.0 w/5-spd that should run for quite a while and still in stock form. Chances are you could find a built 2nd gen Runner w/SAS and an engine swap already for only a few thousand more.
