Trying to decide between Mongoose and Ninja. Thoughts?

Depends on the deck I suppose. What type of deck is it?

A standard Kate deck.

Kate (45 cards)

Kate "Mac" McCaffrey: Digital Tinker

-- Event (0 cards)

3 Diesel

3 Dirty Laundry

3 Infiltration

1 Levy AR Lab Access

2 Modded

2 Special Order

3 Sure Gamble

3 The Maker's Eye

-- Hardware (0 cards)

2 Akamatsu Mem Chip

2 Clone Chip

1 The Toolbox

-- Program (0 cards)

1 Corroder

1 Datasucker

1 Magnum Opus

1 Medium

1 Ninja

2 Self-modifying Code

1 ZU.13 Key Master

-- Resource (0 cards)

1 Aesop's Pawnshop

2 Armitage Codebusting

3 Daily Casts

1 Hunting Grounds

2 Professional Contacts

2 Same Old Thing

1 Technical Writer

Few list comments here.

Why spend the influence on Special Order? Shapers don't need to pull tutors in from other factions with all of their tools that are available.

Any particular reason for Infiltration? I think you card slots could go towards 2 more Techinal Writers and 1 more Self-Modifying Code.

I think Astrolabe would be a better console (2 copies). Toolbox is just...met. If you want a big console, take a look at The Nexus.

Ninja is a pretty bad breaker. I'd go with Mimic, Chameleon, or Atman instead. Oftentimes in Shaper I won't even take a sentry breaker.

Any reason for Aesops? If you are really banking on using it, you'll want 3 copies. With Opus as your main engine, I don't think you'll need it.

This appears to be built with 1 core set, Creation & Control, What Lies Ahead, and Data & Destiny. But yes, another SMC and another Clone Chip (to recur SMC) would be a better use of influence than Special Order. Special Order is Criminal's poor-man's version of Shaper tutoring. This would allow you to run Femme Fatale as a 1x, which should shore up Mongoose's downside nicely. Without an Atman or other sentry options, stacked destroyers could wreck you.

I made some changes I don't have the astrolabe but may look into that set.

Kate 3.0.1 (45 cards)

Kate "Mac" McCaffrey: Digital Tinker

-- event (14 cards)

3 Dirty Laundry

1 Levy AR Lab Access

2 Making an Entrance

2 Modded

3 Sure Gamble

3 The Maker's Eye

-- hardware (6 cards)

2 Clone Chip

3 Sports Hopper

1 The Toolbox

-- program (10 cards)

1 Atman

1 Corroder

1 Datasucker

1 Magnum Opus

1 Medium

1 Mongoose

3 Self-modifying Code

1 ZU.13 Key Master

-- resource (15 cards)

1 Aesop's Pawnshop

2 Armitage Codebusting

3 Daily Casts

3 Patron

2 Professional Contacts

3 Same Old Thing

1 Street Magic

I am also,thinking of swapping toolbox for maya, any suggestions would be great.