There's a difference between "using these sites" and making purchases from those sites. I'll always use these sites as comparison, and then figure out what's getting in the way of getting that fare directly from the airline. (Generally, the difference ends up surfacing that potential "bite" I referred to.)
Having said that, I have found the best source for researching flights to be
ita Software (by Google) Matrix Airfare Search. You cannot purchase airfare that way - it's just a research tool - and it requires a little learning to use particularly well, but it is well worth the investment. It really affords you a rich source of insights into the options available.
For a simpler research tool, I like Google Flights. Again, my intent is to find what I want to purchase, and then purchase it directly from the airline at that fare (or lower).
For hotels, I like to get direct input from previous guests. I get that from comments on the hotels' Facebook pages and from Trip Advisor, the latter of which is where I generally start my search (again, without booking through them - going to the hotel's own booking engine to get the same rate, or better).
As I have gotten older, I'm pulling back from renting a car more and more often, except when driving is the point of the trip (something which actually hasn't happened yet - we do road trips starting from home, not after flying to some other city). Otherwise, I prefer car services. I'm on vacation; let someone else struggle their way through the traffic.