I am looking at traveling on a tour to Israel (Jerusalem, Galilee, Nazareth, Dead Sea, Masada, Tel Aviv and onto Eilat & Petra.

Our choice of dates are March 4-17 $2,600 or April 15-29 $2,800.

Which would be better for good weather and crowds.

The weather should be dramatically better in April. Air temperatures in the low 80sF are typical in the midsection of the country, and rain less likely. Eilat and Dead Sea wil be beginning to be hot, but...
Passover and Easter are over by then, so the biggest crowds will be gone. You will also have just missed Israel Independence Day.

(oops--I mean Israel Independence day will be during the April dates of your trip -I was looking at the wrong calendar!)
It's a very festive day, with most of the country taking to the beaches and parks for barbecues. The day before is Israel's Memorial Day when many activities are curtailed--no movies or theater etc. If you are on a tour, they will be aware of any relevant closings and work around it

We are going on a Smartours April 15-29...which tour operator are you using. Just curious.

The weather is usually nice in March, but there is still a fair chance of rain. It also can rain in April but the odds are much lower. The nights will still be very cool. Other than that there is not much difference considering that you are on an organised tour.