It should be possible to install the Windows SDK on your build server which includes the bootstrapper.
In order to build Visual Studio setup and deployment projects you will need to have VS installed. However, you can use an MSBuild script to build the bootstrapper without VS (a good combination would be to use WiX for your MSI and MSBuild to create the bootstrapper). You will need to use the GenerateBootstrapper task (the following would output a localized bootstrapper installing the .NET Framework):
<Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup>
<BootstrapperFile Include="Microsoft.Net.Framework.2.0">
<ProductName>.NET Framework 2.0</ProductName>
</BootstrapperFile>
<BootstrapperFile Include="Microsoft.Windows.Installer.3.1">
<ProductName>Windows Installer 3.1</ProductName>
</BootstrapperFile>
</ItemGroup>
<Target Name="Bootstrapper">
<GenerateBootstrapper ApplicationFile="mySetup.msi"
Culture="de-DE"
ApplicationName="My Application"
OutputPath="$(OutDir)\de-DE"
BootstrapperItems="@(BootstrapperFile)"
Path="C:\Program Files\Microsoft SDKs\Windows\v6.0A\Bootstrapper\Packages\" />
<GenerateBootstrapper ApplicationFile="mySetup.msi"
Culture="en-US"
ApplicationName="My Application"
OutputPath="$(OutDir)\en-US"
BootstrapperItems="@(BootstrapperFile)"
Path="C:\Program Files\Microsoft SDKs\Windows\v6.0A\Bootstrapper\Packages\" />
</Target>
</Project>
These related questions might be helpful: