It's tricky, I imagine even trickier right now to find a really good tour that can cover the Holy Land*
If you go with something that is sanctioned/facilitated by the state of Israel, you most likely won't have access to places like Bethlehem or most of Jericho, as they are in the West Bank and under PA administration. If you go with something more independently operated, you'll probably get less of a hasbara pitch, but you'll need to listen carefully and mind your p's and q's during entry and exit or it will be a crappy way to start or end your trip.
If you want a religious-focused trip, know that you probably won't get to see some cool stuff and you'll spend a fair amount of time in a tourist bubble with other tour groups. If you go with a tour, one way or another you'll end up with a very sanitized view and wear rose-colored glasses. You'll just have to pick which one works best for you
The best parts there are off the beaten path. I can't recommend time in the West Bank strongly enough- Nablus, Hebron, Jericho, Bethlehem are all amazing, but even finding your way into small villages or wandering around the arab quarter of the Old City deserve to be experienced. Hit up a few Kibbutz in the Negev. I'd say the Golan Heights, but that might be out of the picture these days
Safe enough in the West Bank too. Probably less so than when I was there in early 2010's but still not terrible.
Skip Tel Aviv and go to Jaffa/Yafo. Don't travel halfway around the world to go to a modern european city, go next door to the ocean-front crusader castle
Honestly, might be worth looking for an eco-tour there come to think of it. You could see some really cool stuff and avoid getting sucked into the geopolitics and overt religiousity, while still getting to taste both plenty