If you are using Maven (or Ant) you could add a goal to the deployment phase to copy a file via SCP to your Raspberry Pi. This is described in an example here. Run mvn package to compile your project and copy the output to your Pi in one command. There sould also be a Maven Plugin to use it from inside of Netbeans.
Add something like this to your pom.xml:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-antrun-plugin</artifactId>
<version>1.7</version>
<executions>
<execution>
<id>server-copy</id>
<goals>
<goal>run</goal>
</goals>
<phase>package</phase>
<configuration>
<target>
<echo message="Push to server/home/"/>
<scp trust="yes"
todir="user:password@server:/home/">
<fileset dir="${basedir}/target">
<include name="**/*.jar"/>
</fileset>
</scp>
</target>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant-jsch</artifactId>
<version>1.8.2</version>
</dependency>
</dependencies>
</plugin>