Spacer lifts are fine for mild off road use. Spacers will lift your rig and give you more clearance. The limitation is that they do not provide any additional flex, as do aftermarket options.
The 5100's are longer than stock shocks so you have better flex and more travel which means better performance off road.
If you go with the 5100's, just get the ones for the 2003-2009 4runner. The front will be adjustable from 0"-2.5" lift. For a low budget setup, I'd go with the 5100's, fronts set at 2.5", and a Daystar 1.5" rear spacer. This setup should run under $400.
If you want closer to 3" lift, consider adding FJ coils. You could also add a small top plate spacer, such as the 1/4" spacer Toytec sells.
I've ordered from all these companies before, no complaints. You may be able to find them cheaper elsewhere, but these have very good prices and I know they're legit.
Bilstein 5100 fronts:
Bilstein 24-186711 Monotube Shock Absorber | AJUSA.com
Bilstein 5100 rears:
Bilstein 33-187174 Monotube Shock Absorber | AJUSA.com
Daystar 1.5" spacer:
Daystar Part KT09127BK - ComfortRide Suspension Coil Spring Spacer Kit
1/4" spacer:
Front Top Plate Spacer (One - 1/4") - Toytec Lifts: Toyota Lift Kits: FJ Cruiser Lift Kits, Tacoma Lift Kits, Tundra Lift Kits, 4 Runner Lift Kits, Sequoia Lift Kits, Toyota Truck Lift Kits