An existing, valid, visa waiver does not remove the requirement for ESTA. To fly in you need ESTA. The fact that you already have a visa waiver allowing you to visit for 90 days is irrelevant.
When I made this trip, maybe 3 years ago, I couldn't find anything on the ESTA, or Customs and Border Protection help websites that deals with this situation, and I made the assumption that once your visa waiver is granted, ESTA (which is a precursor to a visa waiver) is superfluous.
ESTA stands for Electronic System for Travel Authorization. The website states that it is a "system to determine if you are eligible to travel to the United States under the Visa Waiver Program without a visa". It would therefore make sense that the fact that a visa waiver has been granted demonstrates that you are eligible for one, removing the need for ESTA.
The US border guard at Toronto airport would not let me board the plane without ESTA. This may just have been his personal interpretation, I cannot say for sure.
This does I suppose match the FAQ on ESTA where it says that you must have ESTA "prior to travelling to the US via air or sea".
The thing that isn't made clear enough anywhere is that a visa waiver is not Travel Authorization, and hence ESTA is still needed to fly.
Elsewhere on the FAQ on ESTA it does say:
The Electronic System for Travel Authorization (ESTA) is an automated system used to determine the eligibility of visitors to travel to the United States under the Visa Waiver Program (VWP) and whether such travel poses any law enforcement or security risk.
Potentially ESTA is therefore still required for the part I have emphasised in bold.