Yes, there's a difference between running and lifting. Mostly, it's in axial loading and the repetition of a force. Studies (the BEST study comes to mind) have shown an increase in BMD in even postmenopausal women from lifting weights; this one validated 8-12 rep max, and others have looked at 15 reps and more with good results.

Running does concentrate gains in BMD in the femur, pelvis, and spine, where we're generally most concerned with fractures associated with age. Lifting gives you gains, but they are more dispersed across the entire body. This, of course, depends on how you lift.

For a well-rounded lifestyle that still gives you a lot of time on the bike, I don't know that you could do better than strength training 2x/wk, running a bit, maybe swimming a little, and cycling to your heart's content.

FWIW, the fears about "wearing out your knees" are not founded on scientific evidence. I'm sure someone will flame this, but if you look, the evidence is just not there; in fact, there's evidence supporting mild impacts and regular movement as being beneficial to collagen synthesis and the nutrition of the cartilage (cartilage is avascular). We're talking about healthy knees here, and moderate running volume. If you're a heavy, overpronating marathoner with a history of meniscus tears, then it's a different story.