She has a shield, so do not worry about her. Stand next to a satellite and wait until your Spidey senses activate. Press LT and dodge, causing her to damage her crystal. Repeat this until she runs away.

In your final encounter with Shriek, she temporarily takes away your Black suit, and figures from your imagination attack you (your loved ones). You can kill them with one hit, but it is pointless. Wait until the Black suit recharges, then switch over, revealing your true enemies. Attack Shriek until she changes you back to the old Spider-Man. Repeat the previous steps and she will collapse.