I was able to build opencv from git (https://github.com/opencv/opencv/tree/3.1.0) using the NDK's cmake yesterday.
export ANDROID_NDK=~/android-sdks/ndk-bundle
cmake -GNinja -DANDROID_TOOLCHAIN_NAME=clang -DANDROID_ABI=armeabi-v7a \
-DANDROID_ARM_NEON=ON -DENABLE_NEON=ON -DANDROID_STL=c++_static \
-DANDROID_CPP_FEATURES="rtti exceptions" -DANDROID_PLATFORM=android-9 \
-DBUILD_ANDROID_EXAMPLES=OFF -DBUILD_DOCS=OFF -DBUILD_FAT_JAVA_LIB=OFF \
-DBUILD_JASPER=OFF -DBUILD_OPENEXR=OFF -DBUILD_PACKAGE=OFF \
-DBUILD_PERF_TESTS=OFF -DBUILD_TESTS=OFF -DBUILD_TIFF=ON \
-DBUILD_WITH_DEBUG_INFO=OFF -DBUILD_opencv_apps=OFF -DBUILD_opencv_java=OFF \
-DBUILD_opencv_python2=OFF -DBUILD_opencv_world=OFF \
-DCMAKE_C_FLAGS_RELEASE="-Os -DNDEBUG -fvisibility=hidden -ffunction-sections -fstack-protector-all" \
-DCMAKE_CXX_FLAGS_RELEASE="-Os -DNDEBUG -fvisibility=hidden -ffunction-sections -fstack-protector-all -fvisibility-inlines-hidden" \
-DENABLE_PRECOMPILED_HEADERS=OFF -DWITH_EIGEN=OFF -DWITH_JASPER=OFF \
-DWITH_OPENEXR=OFF -DWITH_TIFF=ON -DWITH_TBB=ON -DWITH_CUDA=OFF \
-DWITH_CUFFT=OFF -DWITH_WEBP=OFF -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \
-DCMAKE_TOOLCHAIN_FILE=$ANDROID_NDK/build/cmake/android.toolchain.cmake \
path/to/opencv
That's command line use, but something similar should work if you're building from within Android Studio. I'm guessing you don't need all those options, but those were the instructions given to me.
Unfortunately there's a bug in the NDK r13 cmake toolchain that needed to be fixed first: https://github.com/android-ndk/ndk/issues/234. We're about to publish the first beta for NDK r14 which does have the fix. You shouldn't use the betas for production, but if you're not planning to ship right away it should reach stable release in February.