The development, proposed by Hong Kong-based developer Far East Consortium, would involve the demolition of existing buildings on Marsh Wall and Manilla Street, near Canary Wharf, and the construction of three towers of 65, 34 and 20 storeys, which together would provide 634 homes, 231 hotel rooms, a school, a health centre and retail space.
The London Borough of Tower Hamlets resolved in February to refuse planning permission for the scheme, before Johnson wrote to the council last month saying he would determine it.
The council's concerns included the absence of a legal agreement to secure affordable housing and other contributions; concerns of overdevelopment; and lack of an adequate wind assessment.
But a planning report by Greater London Authority (GLA) planners said: "The proposals would introduce a suitable mix of high quality housing types and tenures, including a maximum reasonable amount of affordable housing provision in the context of the viability constraints of developing the site."
It said that 125 of the 634 homes would be classed as affordable.
The report added that the scheme design was of the "highest quality", and that there would be no harm to any heritage assets or strategic views.
Planning obligations were in place for wind mitigation and other issues, it said.
"The scheme is in overall conformity with the Development Plan and constitutes sustainable development," the mayor was told.
