Manage NUGET Packages menu missing after update

Maybe the option wasn't showing because the project was running?

Answer provided by Matt Ward, as taken from the comments:

"The Manage NuGet Packages for Solution menu is the third menu. That is only shown, if a solution is open in Visual Studio 2015. It is also available if you right click the solution in the Solution Explorer."

Another possibility why it is missing is because you haven't created a solution file and just opened the project. Create a solution file and then re-load the solution in Visual Studio (thank you DeveloperDan for this hint).

(Note: The NUGET update I did required a restart of Visual Studio, and when I opened the Tools / Nuget Manager Menu after the restart I did not notice that the solution was closed.)