If the purpose is to have a fast window manager you are certainly better off with C++ or C#, or maybe even Delphi.
But if you are most familiar with Java it can be done.
If you choose the (aging) JNI you would have to write a DLL in C or Delphi that you Java application will use. You should use JNA instead to access the Windows' window handling API functions.
Some of the functions you would use are:
HWND WINAPI GetWindow(HWND hWnd, UINT uCmd);
HWND WINAPI FindWindow(LPCTSTR lpClassName, LPCTSTR lpWindowName);
BOOL WINAPI EnumWindows(WNDENUMPROC lpEnumFunc, LPARAM lParam);
HWND WINAPI WindowFromPoint(POINT Point);
BOOL WINAPI MoveWindow(HWND hWnd, int X, int Y, int nWidth, int nHeight, BOOL bRepaint);
Once you get the window handle (HWND) you can do whatever you like with that window.
EnumWindows function reference at MSDN
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