i thought you were trying to build ns-3 without waf. Qt can build it ,
for instance my Qt directory after building core looks like
John-Abrahams-MacBook-Pro:qtns3 john$ ls
Makefile double.o list-scheduler.o
qtns3.pro string.o unix-fd-reader.o
attribute-construction-list.o enum.o log.o qtns3.pro.user synchronizer.o unix-system-condition.o
attribute.o event-id.o make-event.o random-variable-stream.o system-path.o unix-system-mutex.o
boolean.o event-impl.o map-scheduler.o random-variable.o system-thread.o unix-system-wall-clock-ms.o
breakpoint.o fatal-impl.o names.o realtime-simulator-impl.o test.o vector.o
cairo-wideint.o global-value.o object-base.o ref-count-base.o time.o wall-clock-synchronizer.o
calendar-scheduler.o heap-scheduler.o object-factory.o rng-seed-manager.o timer.o watchdog.o
callback.o hello-simulator.o object-ptr-container.o rng-stream.o trace-source-accessor.o
command-line.o int64x64-128.o object.o scheduler.o type-id.o
config.o int64x64.o pointer.o simulator-impl.o type-name.o
default-simulator-impl.o integer.o
qtns3.app simulator.o uinteger.o
If you trying ns-3 for the first time, I would not recommend building
it without waf.
-john