Justin's solution didn't work for me. Although I could create the x64 platform, x86 stubbornly came back as the only option. My solution is as follows:
(1) Create a new Setup Project for WiX v3.
(2) Close the solution and open the .wixproj file in an extern editor like notepad+.
(3) The file contains only PropertyGroup elements for x86. After that insert the following PropertyGroup elements:
<!-- Insert -->
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x64' ">
<DefineConstants>Debug</DefineConstants>
<OutputPath>bin\$(Platform)\$(Configuration)\</OutputPath>
<IntermediateOutputPath>obj\$(Platform)\$(Configuration)\</IntermediateOutputPath>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|x64' ">
<OutputPath>bin\$(Platform)\$(Configuration)\</OutputPath>
<IntermediateOutputPath>obj\$(Platform)\$(Configuration)\</IntermediateOutputPath>
</PropertyGroup>
(4) Reopen the project. Select Configuration Manager.

Under Project contexts, you can now select x64 in the drop down list. Do it.
(5) The drop down list of Active solution platform still only has x86. Select “New…” In the “New Solution Platform” dialog create the x64 platform.
(6) In the final step synchronize the settings of the solution platform with the project platform so that the four configuration | platform pairs are the same.
Source for step 3: WIX project fails building in X64 platform.