Referring to ​​Build Process of Xamarin.Android​​​, you can find a setting named ​​AndroidSdkBuildToolsVersion​​:

The Android SDK build-tools package provides the ​​aapt​​​ and ​​zipalign​​ tools, among others. Multiple different versions of the build-tools package may be installed simultaneously. The build-tools package chosen for packaging is done by checking for and using a "preferred" build-tools version if it is present; if the "preferred" version is not present, then the highested versioned installed build-tools package is used.

The ​​$(AndroidSdkBuildToolsVersion)​​​ MSBuild property contains the prefered build-tools version. The Xamarin.Android build system provides a default value in ​​Xamarin.Android.Common.targets​​, and the default value may be overridden within youur project file to choose an alternate build-tools version, if (for example) the latest aapt is crashing out while a previous aapt version is known to work.

So, you can change the build-tool version by adding an ​​AndroidSdkBuildToolsVersion​​​ tag under each ​​PropertyGroup​​​ of ​​YourProject.csproj​​ file like below:

  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
    <DebugSymbols>True</DebugSymbols>
    <DebugType>Full</DebugType>
    <Optimize>False</Optimize>
    <OutputPath>bin\Debug\</OutputPath>
    <DefineConstants>DEBUG;TRACE</DefineConstants>
    <ErrorReport>prompt</ErrorReport>
    <WarningLevel>4</WarningLevel>
    <AndroidUseSharedRuntime>True</AndroidUseSharedRuntime>
    <AndroidLinkMode>None</AndroidLinkMode>
    <EmbedAssembliesIntoApk>False</EmbedAssembliesIntoApk>
    <AndroidSdkBuildToolsVersion>24.0.3</AndroidSdkBuildToolsVersion>
  </PropertyGroup>