Android studio Where to install NDK file? (downloaded it in zip)

Download the .zip file. Start the installation through SDK manager.
Go to %userprofile%\AppData\Local\Android\sdk\ndk-bundle and copy .installer folder to desktop and cancel the downloading in SDK manager.
Open .installer folder and open .installationdata file and check the folder in which the file is being downloaded like:
%userprofile%\AppData\Local\Temp\PackageOperation01.
Copy downloaded .zip file to the folder PackageOperation01 or whatever listed in .installationdata file.
Now copy the .installer folder from desktop to %userprofile%\AppData\Local\Android\sdk\ndk-bundle
and start the SDK manager
and start the installation again for NDK.
The SDK manager will start the installation skipping the download process.

Yes, rename the extracted folder android-ndk-r13b(probably the exact name will be outdated someday soon) to ndk-bundle (you can put the NDK [and SDK for that matter] anywhere, and leave the name alone if you want {do not do this, I'm sure seen one case of hard-coded sub-path}),
then, make the settings point to the location where you put it.

Android Studio, File menu | Project Structure Ctrl+Alt+Shift+s
(short-cut: ctrl+Alt+Shift+s):

It might also be helpful to you to set/check the following environmental variables:

NDK_HOME=C:\Android\sdk\ndk-bundle
NDK_MODULE_PATH=C:\Android\sdk\ndk-bundle

EXTRA stuff:

While were doing environmental variables (belt-and-braces for SDK):

ANDROID_HOME=C:\Android\sdk

For JDK:

JAVA_HOME=C:\Program Files\Java\jdk1.8.0_112
JAVA_PATH=C:\Program Files\Java\jre1.8.0_112\bin

JDK is the Java Development Kit.
JRE is the Java Run-time Environment.

If your tight on memory (RAM) for Gradle (700 Megabytes is about as low as you can go, other tools like monitor.bat use this variable too, it's ubiquitous) (clearly you want to make it as big a possible, without swapping making it extremely slow to build {note the underscore VERY important ! [it's a reserved name space conflict operator, don't ask me to explain it's VERY complicated !]}):

_JAVA_OPTIONS=-Xmx700m

Some Links

Setting up for Android NDK development
Add C and C++ Code to Your Project
Getting Started with the NDK
Using C and C++ Code in an Android App with the NDK