I found in many available neural network code implemented using TensorFlow that regularization terms are often implemented by manually adding an additional term to loss valu
As you say in the second point, using the regularizer argument is the recommended way. You can use it in get_variable, or set it once in your variable_scope and have all your variables regularized.
The losses are collected in the graph, and you need to manually add them to your cost function like this.
reg_losses = tf.get_collection(tf.GraphKeys.REGULARIZATION_LOSSES)
reg_constant = 0.01 # Choose an appropriate one.
loss = my_normal_loss + reg_constant * sum(reg_losses)
Hope that helps!