Tested and works with Netbeans 8.2 and Spring-Boot 1.4.3:
First of all make sure you have the Spring Maven plugin included (this should be already included when making a new Netbeans Spring project):
<plugins>
...
<plugin>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>repackage</goal>
</goals>
</execution>
</executions>
</plugin>
...
</plugins>
Also it is a good idea to include the Spring Devtools like this:
<dependencies>
...
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-devtools</artifactId>
</dependency>
...
</dependencies>
Now navigate to your project settings -> Actions -> Debug project and set the following:

Execute goals:
spring-boot:run
Set properties:
run.jvmArguments=-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address}
jpda.listen=true
Now run your application via the usual debug button and Spring should properly connect to the JVM debugger.
Spring Boot 2.x
To enable Netbeans debugging for a Spring Boot 2.x project (and more specifically version 2.x of the spring-boot-maven-plugin) the procedure is exactly the same, except the run.jvmArguments
property name has changed to spring-boot.run.jvmArguments
:
spring-boot.run.jvmArguments=-Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=${jpda.address}
jpda.listen=true