Custom table naming/access convention for multisite: $table_prefix vs base_prefix or other?

After WP3.8.1 upgraded, two plugins I made for my networks both stopped working. Each runs on a separate multisite install. I posted the error report on the WordPress form: http://wordpress.org/support/topic/table_prefix-error-since-wp-381-upgrade?replies=1

For Multisite, is there a better way of accessing my custom table than using
$my_custom_table = $wpdb->$table_prefix.'my_custom_table';?
I see here the use of base_prefix: http://wordpress.org/support/topic/multisite-table-prefix-wpdb-prefix-incorrect?replies=6

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Would it be better to rename my custom table as
wp_my_custom_table, instead of

my_custom_table, and use
$my_custom_table = $wpdb->base_prefix('my_custom_table');.

This outputs wp_my_custom_table.

Or are there advantages to leaving the table name as is, using $table_prefix, and waiting for the error report to be resolved?

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