Never register your domain with the same company / account you have your hosting under. If you keep them independent and something catastrophic happens to your servers you'll still be able point the domain(s) somewhere else. If AWS goes down and takes the control panel with it you won't be able to do anything with your domain.
Unfortunately the TTL settings on top-level zones are less than friendly if your goal is to withstand a DNS provider outage by changing the registration. The TTLs on NS records in the ".com" zone are two days long. So when you log in to your registrar of choice and change the delegation, it's still going to be two days before all resolvers are using your new choice. You can improve things for most resolvers, by lowering the NS TTLs in your child-zone (though few do), but about 10% of resolvers are "parent-centric" and you'll just have to wait the two days.
Using multiple providers, but using no more than two authoritative nameservers from each provider [1], is probably the way to go if your goal is to withstand a full-provider DNS outage. Unfortunately when you do that, you have to also consider that if DNS is your tool for handling day-to-day problems like web-server failures; then every time you need to make a DNS change, you need all of your providers to reflect it reliably and quickly.
Or put another way; using multiple providers can lower your day to day availability, because of the increased probability that at least one of your providers is slow to make changes when you need it.
Full disclosure: I work on Route 53.
[1] Most resolvers will try 3 different name servers before giving up, so if you have 3 or more from any one provider in can be ineffective.
