We did the observatory a few months after it opened. Had dinner up there. Would not recommend it though. Poor service, food was bland, and very expensive. I know you said your wife was afraid of heights, so I need to tell you she might be bothered up there. If you do decide to go up top, pay for the upgrade to pass the line. It gets long, and does not move at healthy pace.
You might have your fill of boat rides going to the Statue and Ellis Island, but if not, I definitely agree with Red’s recommendation of taking the free Staten Island Ferry. Nice relaxing and scenic. Just try to avoid it at rush hour.